Gene/Protein Disease Symptom Drug Enzyme Compound
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Query: UMLS:C0019693 (HIV)
 170,526 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

The HIV-1 integrase, which is essential for viral replication, catalyzes the insertion of viral DNA into the host chromosome thereby recruiting host cell machinery into making viral proteins. It represents the third main HIV enzyme target for inhibitor design, the first two being the reverse transcriptase and the protease. We report here a fully hydrated 2 ns molecular dynamics simulation performed using parallel NWChem3.2.1 with the AMBER95 force field. The HIV-1 integrase catalytic domain previously determined by crystallography (1B9D) and modeling including two Mg(2+) ions placed into the active site based on an alignment against an ASV integrase structure containing two divalent metals (1VSH), was used as the starting structure. The simulation reveals a high degree of flexibility in the region of residues 140-149 even in the presence of a second divalent metal ion and a dramatic conformational change of the side chain of E152 when the second metal ion is present. This study shows similarities in the behavior of the catalytic residues in the HIV-1 and ASV integrases upon metal binding. The present simulation also provides support to the hypothesis that the second metal ion is likely to be carried into the HIV-1 integrase active site by the substrate, a strand of DNA.
Biopolymers 2000 Apr 05
PMID:Similarities in the HIV-1 and ASV integrase active sites upon metal cofactor binding. 1068 51

Nanosecond molecular dynamics simulations in a fully solvated phospholipid bilayer have been performed on single transmembrane alpha-helices from three putative ion channel proteins encoded by viruses: NB (from influenza B), CM2 (from influenza C), and Vpu (from HIV-1). alpha-Helix stability is maintained within a core region of ca. 28 residues for each protein. Helix perturbations are due either to unfavorable interactions of hydrophobic residues with the lipid headgroups or to the need of the termini of short helices to extend into the surrounding interfacial environment in order to form H-bonds. The requirement of both ends of a helix to form favorable interactions with lipid headgroups and/or water may also lead to tilting and/or kinking of a transmembrane alpha-helix. Residues that are generally viewed as poor helix formers in aqueous solution (e.g., Gly, Ile, Val) do not destabilize helices, if located within a helix that spans a lipid bilayer. However, helix/bilayer mismatch such that a helix ends abruptly within the bilayer core destabilizes the end of the helix, especially in the presence of Gly and Ala residues. Hydrogen bonding of polar side-chains with the peptide backbone and with one another occurs when such residues are present within the bilayer core, thus minimizing the energetic cost of burying such side-chains.
Biopolymers 2000 Jun
PMID:Transmembrane domains of viral ion channel proteins: a molecular dynamics simulation study. 1076 49

The Food and Drug Administration (FDA) recently approved Ribavirin capsules as a part of combination therapy for treating chronic hepatitis C in patients with certain conditions. The drug will be called Rebetol, and will be distributed by Schering-Plough. Oral Ribavirin has been used in the rest of the world as an antiviral, but its use in the United States was not approved by the FDA. Recent studies suggest the drug may have considerable importance in treating HIV.
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PMID:Ribavirin approved for hepatitis C combination treatment. 1136 95

Thymosin-Alpha-1 (Zadaxin) is a synthetic hormone that has been studied as a treatment for HIV, hepatitis B, and hepatitis C. Recently approved in Mexico as a booster for the flu vaccine, it was also approved in nine other countries for flu, hepatitis B, and hepatitis C. The demand for Thymosin is great but it is difficult to procure. A partnership between Schering-Plough and SciClone Pharmaceuticals has renewed hope that the demand for Thymosin will be met. Schering-Plough is also marketing Rebetron, a packaged combination of Ribavirin capsules and injectable alpha-interferon (Intron-A), for the treatment of hepatitis C. Other hepatitis treatments are described, such as Epivir-HBV (3TC, Epivir) which was approved in December for the treatment of Hepatitis B. Epivir-HBV has shown promising results.
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PMID:Hepatitis treatment update: new approvals, not much news. 1136 97

Ribavirin (Rebetol) is Schering Corporation's newly approved drug. It is used in combination with interferon for treatment of chronic hepatitis C in patients whose compensated liver disease has not been treated or who have relapsed after interferon monotherapy. Results of clinical trials are summarized, and dosing options and side effects are detailed. Similar information is provided for abacavir (Ziagen), Glaxo-Wellcome's new nucleoside analog reverse transcriptase inhibitor (NRTI) that is used in combination therapy to treat HIV.
Hopkins HIV Rep 1999 Mar
PMID:Product information. 1136 50

Phosphorylation and dephosphorylation are key events in protein expression and regulation and in signal transduction. Phosphopeptides are very useful reagents for the study of these processes, and have been used to great advantage in the study of phosphatase substrate specificity, SH2 domain ligand specificity, and protein-protein interactions. Furthermore, the advent of cell-permeable peptide carriers, such as those from the antennapedia homeodomain and the HIV TAT transcription factor, has allowed the study of intracellular events, thus underscoring the utility of these reagents. In this paper we review methods for the synthesis of phosphopeptides with the emphasis on the preparation of phosphoamino acid building blocks.
Biopolymers 2001
PMID:The synthesis of phosphopeptides. 1137 30

As the prevalence of AIDS continues to grow, and current therapeutic agents begin to lose efficacy, the need for alternative treatments to combat HIV has become significantly greater. Targeting the highly conserved dimerization interface of HIV protease (PR) with interfacial peptides has been shown to reduce the activity of the enzyme due to generation of inactive monomers. The potency of these peptide-based inhibitors has been dramatically increased by cross-linking the interfacial sequences derived from HIV PR. This review focuses on a variety of strategies to develop potent, low-molecular-weight dimerization inhibitors of HIV PR.
Biopolymers 2002
PMID:Novel strategies for targeting the dimerization interface of HIV protease with cross-linked interfacial peptides. 1232 62

We present a model structure of a candidate tetramer for HIV-1 integrase. The model was built in three steps using data from fluorescence anisotropy, structures of the individual integrase domains, cross-linking data, and other biochemical data. First, the structure of the full-length integrase monomer was modeled using the individual domain structures and the hydrodynamic properties of the full-length protein that were recently measured by fluorescence depolarization. We calculated the rotational correlation times for different arrangements of three integrase domains, revealing that only structures with close proximity among the domains satisfied the experimental data. The orientations of the domains were constrained by iterative tests against the data on cross-linking and footprinting in integrase-DNA complexes. Second, the structure of an integrase dimer was obtained by joining the model monomers in accordance with the available dimeric crystal structures of the catalytic core. The hydrodynamic properties of the dimer were in agreement with the experimental values. Third, the active sites of the two model dimers were placed in agreement with the spacing between the sites of integration on target DNA as well as the integrase-DNA cross-linking data, resulting in twofold symmetry of a tetrameric complex. The model is consistent with the experimental data indicating that the F185K substitution, which is found in the model at a tetramerization interface, selectively disrupts correct complex formation in vitro and HIV replication in vivo. Our model of the integrase tetramer bound to DNA may help to design anti-integrase inhibitors.
Biopolymers 2003 Jan
PMID:Modeling HIV-1 integrase complexes based on their hydrodynamic properties. 1257 83

Pegylation of interferon-alpha-2a is associated with improved sustained virological response rates in patients with chronic hepatitis C. Subsequently, combination therapy with peginterferon-alpha-2a (40kD) [Pegasys] and ribavirin (Copegus trade mark, Rebetol) was investigated to establish if the efficacy of peginterferon-alpha-2a (40kD) monotherapy could be further enhanced. Subcutaneous peginterferon-alpha-2a (40kD) was administered at a dosage of 180 micro g once weekly and oral ribavirin was usually administered at a dosage of 1000 or 1200 mg/day. In treatment-naive patients with chronic hepatitis C, the sustained virological response rate (assessed 24 weeks after the end of a 48-week treatment period) was significantly higher in peginterferon-alpha-2a (40kD) plus ribavirin recipients than in peginterferon-alpha-2a (40kD) plus placebo recipients or interferon-alpha-2b plus ribavirin recipients (56% vs 29% and 44%). Retrospective analysis revealed that peginterferon-alpha-2a (40kD) plus ribavirin recipients who did not achieve an early virological response were unlikely to achieve a sustained response. Treatment with peginterferon-alpha-2a (40kD) plus another antiviral agent (ribavirin, mycophenolate mofetil, amantadine, or ribavirin and amantadine) was beneficial in patients with chronic hepatitis C who had relapsed during or after, or had not responded to, treatment with interferon-alpha-2b plus ribavirin. In the relapse study, sustained virological response rates in recipients of peginterferon-alpha-2a (40kD) plus ribavirin were 45% with and 38% without amantadine. Peginterferon-alpha-2a (40kD) plus ribavirin appears beneficial in patients with chronic hepatitis C considered difficult to treat (e.g. patients infected with hepatitis C virus genotype 4, African-American patients, patients with advanced fibrosis or cirrhosis and patients co-infected with HIV). Flu-like symptoms and depression occurred significantly less frequently with peginterferon-alpha-2a (40kD) plus ribavirin than with interferon-alpha-2b plus ribavirin. Similar proportions of patients receiving peginterferon-alpha-2a (40kD) plus ribavirin, peginterferon-alpha-2a (40kD) plus placebo and interferon-alpha-2b plus ribavirin withdrew from treatment because of laboratory abnormalities or other adverse events. In conclusion, combination therapy comprising subcutaneous peginterferon-alpha-2a (40kD) and oral ribavirin is an important new treatment option for chronic hepatitis C. Peginterferon-alpha-2a (40kD) plus oral ribavirin is significantly more effective than peginterferon-alpha-2a (40kD) monotherapy or interferon-alpha-2b plus ribavirin at inducing a sustained virological response in treatment-naive patients with chronic hepatitis C. Preliminary data suggest that peginterferon-alpha-2a (40kD) plus ribavirin is also beneficial in treatment-experienced patients and in patients who have traditionally been considered difficult to treat. Combination therapy with peginterferon-alpha-2a (40kD) and oral ribavirin is poised to become a valuable first-line treatment option in chronic hepatitis C.
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PMID:Peginterferon-alpha-2a (40kD) plus ribavirin: a review of its use in the management of chronic hepatitis C. 1265 50

A mode-coupling solution of the Smoluchowski diffusion equation (MCD theory), designed to describe the dynamics of wobbling macromolecules in water, is applied to a macromolecular bead model including water beads in the nearest layers. The necessary statistical averages are evaluated by time averaging along a molecular dynamics (MD) trajectory where both solute and water are introduced as atomistic models. The cross peaks in (1)H nuclear Overhauser effect spectroscopy (NOESY) NMR spectra that are routinely measured to determine biological structures are here calculated for the mutated 23 nucleotides stem-loop fragment of the SL1 domain in the HIV-1(Lai) genomic RNA. The calculations are in acceptable agreement with experiments without requiring any screening of the hydrodynamic interactions. The screening of hydrodynamics was necessary in previous MCD calculations obtained by using the same full atomistic MD trajectory, but a nonsolvated frictional model.
Biopolymers 2003 May
PMID:Modeling the dynamics of the solvated SL1 domain of HIV-1 genomic RNA. 1271 18


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